Entering edit mode
10.5 years ago
biohack92
▴
170
Just need confirmation of whether I am constructing the correct design matrix
I am working with 2-color Agilent arrays. I've bg-corrected and normalized the expression values. The goal of the experiment is to see if there's differential expression between pre-treatment and post-treatment with a drug.
The microarrays were formatted as follows:
pre = pre- drug treatment
post = post- drug treatment
file Cy3 Cy5
Array 1 file1.txt pre pre
Array 2 file2.txt pre post
Array 3 file3.txt pre pre
Array 4 file4.txt post pre
Array 5 file5.txt post pre
Array 6 file6.txt pre post
Is design <- modelMatrix(targets, ref="pre")
an accurate design matrix? or does the pre
-pre
arrays need separate analysis?
Any guidance would be appreciated.